diff --git a/CHANGELOG.md b/CHANGELOG.md
index e4ab2e523fa..f11c9077400 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,14 @@
 # rollup changelog
 
+## 2.0.6
+*2020-03-13*
+
+### Bug Fixes
+* Do not use file names from different outputs when generating sourcemaps using the `dir` option (#3440)
+
+### Pull Requests
+* [#3440](https://github.com/rollup/rollup/pull/3440): Use correct file names when writing sourcemaps for multiple outputs (@lukastaegert)
+
 ## 2.0.5
 *2020-03-12*
 
diff --git a/docs/05-plugin-development.md b/docs/05-plugin-development.md
index 0ae2b48fb7f..51544787d48 100644
--- a/docs/05-plugin-development.md
+++ b/docs/05-plugin-development.md
@@ -413,7 +413,7 @@ resolveImportMeta(property, {moduleId}) {
 Note that since this hook has access to the filename of the current chunk, its return value will not be considered when generating the hash of this chunk.
 
 #### `writeBundle`
-Type: `( bundle: { [fileName: string]: AssetInfo | ChunkInfo }) => void`<br>
+Type: `(options: OutputOptions, bundle: { [fileName: string]: AssetInfo | ChunkInfo }) => void`<br>
 Kind: `async, parallel`<br>
 Previous Hook: [`generateBundle`](guide/en/#generatebundle)<br>
 Next Hook: If it is called, this is the last hook of the output generation phase and may again be followed by [`outputOptions`](guide/en/#outputoptions) if another output is generated.
diff --git a/package-lock.json b/package-lock.json
index 742a10ad83a..405683a6844 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "rollup",
-  "version": "2.0.5",
+  "version": "2.0.6",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
diff --git a/package.json b/package.json
index bdc7936a829..44e415d1394 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "rollup",
-  "version": "2.0.5",
+  "version": "2.0.6",
   "description": "Next-generation ES module bundler",
   "main": "dist/rollup.js",
   "module": "dist/es/rollup.js",
diff --git a/src/Chunk.ts b/src/Chunk.ts
index ecd64cbc207..4c126ef256e 100644
--- a/src/Chunk.ts
+++ b/src/Chunk.ts
@@ -509,6 +509,7 @@ export default class Chunk {
 	) {
 		timeStart('render format', 3);
 
+		const chunkId = this.id!;
 		const format = options.format as string;
 		const finalise = finalisers[format];
 		if (options.dynamicImportFunction && format !== 'es') {
@@ -602,12 +603,12 @@ export default class Chunk {
 
 				let file: string;
 				if (options.file) file = resolve(options.sourcemapFile || options.file);
-				else if (options.dir) file = resolve(options.dir, this.id!);
-				else file = resolve(this.id!);
+				else if (options.dir) file = resolve(options.dir, chunkId);
+				else file = resolve(chunkId);
 
 				const decodedMap = magicString.generateDecodedMap({});
 				map = collapseSourcemaps(
-					this,
+					this.graph,
 					file,
 					decodedMap,
 					this.usedModules,
diff --git a/src/utils/collapseSourcemaps.ts b/src/utils/collapseSourcemaps.ts
index 8e310f7362a..b347bcde603 100644
--- a/src/utils/collapseSourcemaps.ts
+++ b/src/utils/collapseSourcemaps.ts
@@ -1,5 +1,4 @@
 import { DecodedSourceMap, SourceMap } from 'magic-string';
-import Chunk from '../Chunk';
 import Graph from '../Graph';
 import Module from '../Module';
 import {
@@ -200,14 +199,14 @@ function getCollapsedSourcemap(
 }
 
 export function collapseSourcemaps(
-	bundle: Chunk,
+	graph: Graph,
 	file: string,
 	map: DecodedSourceMap,
 	modules: Module[],
 	bundleSourcemapChain: DecodedSourceMapOrMissing[],
 	excludeContent: boolean | undefined
 ) {
-	const linkMap = getLinkMap(bundle.graph);
+	const linkMap = getLinkMap(graph);
 	const moduleSources = modules
 		.filter(module => !module.excludeFromSourcemap)
 		.map(module =>
diff --git a/test/cli/samples/config-multiple-source-maps/_config.js b/test/cli/samples/config-multiple-source-maps/_config.js
new file mode 100644
index 00000000000..a91d466ccdc
--- /dev/null
+++ b/test/cli/samples/config-multiple-source-maps/_config.js
@@ -0,0 +1,4 @@
+module.exports = {
+	description: 'correctly generates sourcemaps for multiple outputs',
+	command: 'rollup -c'
+};
diff --git a/test/cli/samples/config-multiple-source-maps/_expected/main-cjs.js b/test/cli/samples/config-multiple-source-maps/_expected/main-cjs.js
new file mode 100644
index 00000000000..a93f480e14c
--- /dev/null
+++ b/test/cli/samples/config-multiple-source-maps/_expected/main-cjs.js
@@ -0,0 +1,4 @@
+'use strict';
+
+assert.equal( ANSWER, 42 );
+//# sourceMappingURL=main-cjs.js.map
diff --git a/test/cli/samples/config-multiple-source-maps/_expected/main-cjs.js.map b/test/cli/samples/config-multiple-source-maps/_expected/main-cjs.js.map
new file mode 100644
index 00000000000..086c5841cee
--- /dev/null
+++ b/test/cli/samples/config-multiple-source-maps/_expected/main-cjs.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"main-cjs.js","sources":["../main.js"],"sourcesContent":["assert.equal( ANSWER, 42 );\n"],"names":[],"mappings":";;AAAA,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,EAAE"}
\ No newline at end of file
diff --git a/test/cli/samples/config-multiple-source-maps/_expected/main-es.js b/test/cli/samples/config-multiple-source-maps/_expected/main-es.js
new file mode 100644
index 00000000000..8d97b6cf48d
--- /dev/null
+++ b/test/cli/samples/config-multiple-source-maps/_expected/main-es.js
@@ -0,0 +1,2 @@
+assert.equal( ANSWER, 42 );
+//# sourceMappingURL=main-es.js.map
diff --git a/test/cli/samples/config-multiple-source-maps/_expected/main-es.js.map b/test/cli/samples/config-multiple-source-maps/_expected/main-es.js.map
new file mode 100644
index 00000000000..931e92a9cde
--- /dev/null
+++ b/test/cli/samples/config-multiple-source-maps/_expected/main-es.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"main-es.js","sources":["../main.js"],"sourcesContent":["assert.equal( ANSWER, 42 );\n"],"names":[],"mappings":"AAAA,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,EAAE"}
\ No newline at end of file
diff --git a/test/cli/samples/config-multiple-source-maps/main.js b/test/cli/samples/config-multiple-source-maps/main.js
new file mode 100644
index 00000000000..df16c1b06b9
--- /dev/null
+++ b/test/cli/samples/config-multiple-source-maps/main.js
@@ -0,0 +1 @@
+assert.equal( ANSWER, 42 );
diff --git a/test/cli/samples/config-multiple-source-maps/rollup.config.js b/test/cli/samples/config-multiple-source-maps/rollup.config.js
new file mode 100644
index 00000000000..db2092f239e
--- /dev/null
+++ b/test/cli/samples/config-multiple-source-maps/rollup.config.js
@@ -0,0 +1,17 @@
+export default {
+	input: 'main.js',
+	output: [
+		{
+			format: 'cjs',
+			dir: '_actual',
+			entryFileNames: '[name]-[format].js',
+			sourcemap: true,
+		},
+		{
+			format: 'es',
+			dir: '_actual',
+			entryFileNames: '[name]-[format].js',
+			sourcemap: true
+		}
+	]
+};